############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SIM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SIM_1.76.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIM.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SIM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘SIM’ version ‘1.76.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SIM’ can be installed ... OK * used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘biomaRt’ in package code. Please use :: or requireNamespace() instead. See section 'Suggested packages' in the 'Writing R Extensions' manual. Package in Depends field not imported from: ‘quantreg’ These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘SIM/R/zzz.R’: .onAttach calls: library.dynam("SIM", pkg, lib) See section ‘Good practice’ in '?.onAttach'. dependent.heatmap: warning in get(as.character(adjust[[2]]), env = attr(adjust, ".Environment")): partial argument match of 'env' to 'envir' sim.plot.zoom.in: warning in eval(call, env = attr(call, "env")): partial argument match of 'env' to 'envir' sim.update.chrom.table: warning in factor(table$name, level = c(1:22, "X", "Y")): partial argument match of 'level' to 'levels' assemble.data: no visible binding for global variable ‘chrom.table’ convertGenomicRegion: no visible binding for global variable ‘chrom.table’ dependent.heatmap: no visible global function definition for ‘strwidth’ getoverlappingregions: no visible global function definition for ‘useMart’ getoverlappingregions: no visible global function definition for ‘getBM’ independent.heatmap: no visible global function definition for ‘strwidth’ link.metadata: no visible binding for global variable ‘expr.data’ link.metadata: no visible binding for global variable ‘hgu133plus2CHR’ link.metadata: no visible binding for global variable ‘hgu133plus2CHRLOC’ link.metadata: no visible binding for global variable ‘hgu133plus2SYMBOL’ plotCytobands: no visible binding for global variable ‘chrom.table’ sim.plot.overlapping.indep.dep.features: no visible global function definition for ‘box’ sim.plot.pvals.on.genome: no visible binding for global variable ‘chrom.table’ sim.update.chrom.table: no visible global function definition for ‘dbConnect’ sim.update.chrom.table: no visible global function definition for ‘MySQL’ sim.update.chrom.table: no visible global function definition for ‘dbGetQuery’ Undefined global functions or variables: MySQL box chrom.table dbConnect dbGetQuery expr.data getBM hgu133plus2CHR hgu133plus2CHRLOC hgu133plus2SYMBOL strwidth useMart Consider adding importFrom("graphics", "box", "strwidth") to your NAMESPACE file. * checking Rd files ... WARNING checkRd: (5) integrated.analysis.Rd:116: \item in \value must have non-empty label * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed SIM-package 15.347 0.475 16.061 integrated.analysis 12.338 0.072 12.850 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/SIM.Rcheck/00check.log’ for details.